Literature DB >> 29092945

The Digital Slide Archive: A Software Platform for Management, Integration, and Analysis of Histology for Cancer Research.

David A Gutman1,2,3, Mohammed Khalilia4, Sanghoon Lee4, Michael Nalisnik2, Zach Mullen5, Jonathan Beezley5, Deepak R Chittajallu5, David Manthey5, Lee A D Cooper2,3,6.   

Abstract

Tissue-based cancer studies can generate large amounts of histology data in the form of glass slides. These slides contain important diagnostic, prognostic, and biological information and can be digitized into expansive and high-resolution whole-slide images using slide-scanning devices. Effectively utilizing digital pathology data in cancer research requires the ability to manage, visualize, share, and perform quantitative analysis on these large amounts of image data, tasks that are often complex and difficult for investigators with the current state of commercial digital pathology software. In this article, we describe the Digital Slide Archive (DSA), an open-source web-based platform for digital pathology. DSA allows investigators to manage large collections of histologic images and integrate them with clinical and genomic metadata. The open-source model enables DSA to be extended to provide additional capabilities. Cancer Res; 77(21); e75-78. ©2017 AACR. ©2017 American Association for Cancer Research.

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Year:  2017        PMID: 29092945      PMCID: PMC5898232          DOI: 10.1158/0008-5472.CAN-17-0629

Source DB:  PubMed          Journal:  Cancer Res        ISSN: 0008-5472            Impact factor:   12.701


  6 in total

1.  The molecular basis of breast cancer pathological phenotypes.

Authors:  Yujing J Heng; Susan C Lester; Gary Mk Tse; Rachel E Factor; Kimberly H Allison; Laura C Collins; Yunn-Yi Chen; Kristin C Jensen; Nicole B Johnson; Jong Cheol Jeong; Rahi Punjabi; Sandra J Shin; Kamaljeet Singh; Gregor Krings; David A Eberhard; Puay Hoon Tan; Konstanty Korski; Frederic M Waldman; David A Gutman; Melinda Sanders; Jorge S Reis-Filho; Sydney R Flanagan; Deena Ma Gendoo; Gregory M Chen; Benjamin Haibe-Kains; Giovanni Ciriello; Katherine A Hoadley; Charles M Perou; Andrew H Beck
Journal:  J Pathol       Date:  2016-12-29       Impact factor: 7.996

2.  Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association.

Authors:  Hang Chang; Ju Han; Alexander Borowsky; Leandro Loss; Joe W Gray; Paul T Spellman; Bahram Parvin
Journal:  IEEE Trans Med Imaging       Date:  2012-12-04       Impact factor: 10.048

3.  Standardization in digital pathology: Supplement 145 of the DICOM standards.

Authors:  Rajendra Singh; Lauren Chubb; Liron Pantanowitz; Anil Parwani
Journal:  J Pathol Inform       Date:  2011-05-11

Review 4.  Novel genotype-phenotype associations in human cancers enabled by advanced molecular platforms and computational analysis of whole slide images.

Authors:  Lee A D Cooper; Jun Kong; David A Gutman; William D Dunn; Michael Nalisnik; Daniel J Brat
Journal:  Lab Invest       Date:  2015-01-19       Impact factor: 5.662

5.  Identifying survival associated morphological features of triple negative breast cancer using multiple datasets.

Authors:  Chao Wang; Thierry Pécot; Debra L Zynger; Raghu Machiraju; Charles L Shapiro; Kun Huang
Journal:  J Am Med Inform Assoc       Date:  2013-04-12       Impact factor: 4.497

6.  Machine-based morphologic analysis of glioblastoma using whole-slide pathology images uncovers clinically relevant molecular correlates.

Authors:  Jun Kong; Lee A D Cooper; Fusheng Wang; Jingjing Gao; George Teodoro; Lisa Scarpace; Tom Mikkelsen; Matthew J Schniederjan; Carlos S Moreno; Joel H Saltz; Daniel J Brat
Journal:  PLoS One       Date:  2013-11-13       Impact factor: 3.240

  6 in total
  37 in total

1.  Open access image repositories: high-quality data to enable machine learning research.

Authors:  F Prior; J Almeida; P Kathiravelu; T Kurc; K Smith; T J Fitzgerald; J Saltz
Journal:  Clin Radiol       Date:  2019-04-28       Impact factor: 2.350

Review 2.  Enhancing the Value of Histopathological Assessment of Allograft Biopsy Monitoring.

Authors:  Michelle A Wood-Trageser; Andrew J Lesniak; Anthony J Demetris
Journal:  Transplantation       Date:  2019-07       Impact factor: 4.939

3.  Quantitative digital histopathology and machine learning to predict pathological complete response to chemotherapy in breast cancer patients using pre-treatment tumor biopsies.

Authors:  Khadijeh Saednia; Andrew Lagree; Marie A Alera; Lauren Fleshner; Audrey Shiner; Ethan Law; Brianna Law; David W Dodington; Fang-I Lu; William T Tran; Ali Sadeghi-Naini
Journal:  Sci Rep       Date:  2022-06-11       Impact factor: 4.996

4.  Risk of Subsequent Cutaneous Melanoma in Moderately Dysplastic Nevi Excisionally Biopsied but With Positive Histologic Margins.

Authors:  Caroline C Kim; Elizabeth G Berry; Michael A Marchetti; Susan M Swetter; Geoffrey Lim; Douglas Grossman; Clara Curiel-Lewandrowski; Emily Y Chu; Michael E Ming; Kathleen Zhu; Meera Brahmbhatt; Vijay Balakrishnan; Michael J Davis; Zachary Wolner; Nathaniel Fleming; Laura K Ferris; John Nguyen; Oleksandr Trofymenko; Yuan Liu; Suephy C Chen
Journal:  JAMA Dermatol       Date:  2018-12-01       Impact factor: 10.282

Review 5.  Artificial intelligence and algorithmic computational pathology: an introduction with renal allograft examples.

Authors:  Alton B Farris; Juan Vizcarra; Mohamed Amgad; Lee A D Cooper; David Gutman; Julien Hogan
Journal:  Histopathology       Date:  2021-03-08       Impact factor: 5.087

6.  User friendly, cloud based, whole slide image segmentation.

Authors:  Brendon Lutnick; Avinash Kammardi Shashiprakash; David Manthey; Pinaki Sarder
Journal:  Proc SPIE Int Soc Opt Eng       Date:  2021-02-15

7.  Automated Computational Detection of Interstitial Fibrosis, Tubular Atrophy, and Glomerulosclerosis.

Authors:  Brandon Ginley; Kuang-Yu Jen; Seung Seok Han; Luís Rodrigues; Sanjay Jain; Agnes B Fogo; Jonathan Zuckerman; Vighnesh Walavalkar; Jeffrey C Miecznikowski; Yumeng Wen; Felicia Yen; Donghwan Yun; Kyung Chul Moon; Avi Rosenberg; Chirag Parikh; Pinaki Sarder
Journal:  J Am Soc Nephrol       Date:  2021-02-23       Impact factor: 10.121

8.  PodoSighter: A Cloud-Based Tool for Label-Free Podocyte Detection in Kidney Whole-Slide Images.

Authors:  Darshana Govind; Jan U Becker; Jeffrey Miecznikowski; Avi Z Rosenberg; Julien Dang; Pierre Louis Tharaux; Rabi Yacoub; Friedrich Thaiss; Peter F Hoyer; David Manthey; Brendon Lutnick; Amber M Worral; Imtiaz Mohammad; Vighnesh Walavalkar; John E Tomaszewski; Kuang-Yu Jen; Pinaki Sarder
Journal:  J Am Soc Nephrol       Date:  2021-09-03       Impact factor: 10.121

9.  A Distributed System Improves Inter-Observer and AI Concordance in Annotating Interstitial Fibrosis and Tubular Atrophy.

Authors:  Avinash Kammardi Shashiprakash; Brendon Lutnick; Brandon Ginley; Darshana Govind; Nicholas Lucarelli; Kuang-Yu Jen; Avi Z Rosenberg; Anatoly Urisman; Vighnesh Walavalkar; Jonathan E Zuckerman; Marco Delsante; Mei Lin Z Bissonnette; John E Tomaszewski; David Manthey; Pinaki Sarder
Journal:  Proc SPIE Int Soc Opt Eng       Date:  2021-02-15

10.  Image Analysis Pipeline for Renal Allograft Evaluation and Fibrosis Quantification.

Authors:  Alton Brad Farris; Juan Vizcarra; Mohamed Amgad; Lee Alex Donald Cooper; David Gutman; Julien Hogan
Journal:  Kidney Int Rep       Date:  2021-04-24
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